Atomistic Free Energy Model for Nucleic Acids: Simulations of Single-Stranded DNA and the Entropy Landscape of RNA Stem–Loop Structures

2015 ◽  
Vol 119 (47) ◽  
pp. 14840-14856 ◽  
Author(s):  
Chi H. Mak
Keyword(s):  
Free Energy ◽  
Nucleic Acids ◽  
Energy Model ◽  
Single Stranded Dna ◽  
Stem Loop ◽  
Free Energy Model

Hydrogen Atom Transfer Reaction Free Energy as a Predictor of Abiotic Nitroaromatic Reduction Rate Constants: A Comprehensive Analysis

2019 ◽  
Author(s):  
Dominic Di Toro ◽  
Kevin P. Hickey ◽  
Herbert E. Allen ◽  
Richard F. Carbonaro ◽  
Pei C. Chiu
Keyword(s):  
Free Energy ◽  
Hydrogen Atom ◽  
Hydrogen Atom Transfer ◽  
Energy Model ◽  
Second Order ◽  
Transfer Model ◽  
Atom Transfer ◽  
Order Rate ◽  
Linear Free Energy ◽  
Free Energy Model

<div>A linear free energy model is presented that predicts the second order rate constant for the abiotic reduction of nitroaromatic compounds (NACs). For this situation previously presented models use the one electron reduction potential of the NAC reaction. If such value is not available, it has been has been proposed that it could be computed directly or estimated from the electron affinity (EA). The model proposed herein uses the Gibbs free energy of the hydrogen atom transfer (HAT) as the parameter in the linear free energy model. Both models employ quantum chemical computations for the required thermodynamic parameters. The available and proposed models are compared using second order rate constants obtained from five investigations reported in the literature in which a variety of NACs were exposed to a variety of reductants. A comprehensive analysis utilizing all the NACs and reductants demonstrate that the computed hydrogen atom transfer model and the experimental one electron reduction potential model have similar root mean square errors and residual error probability distributions. In contrast, the model using the computed electron affinity has a more variable residual error distribution with a significant number of outliers. The results suggest that a linear free energy model utilizing computed hydrogen transfer reaction free energy produces a more reliable prediction of the NAC abiotic reduction second order rate constant than previously available methods. The advantages of the proposed hydrogen atom transfer model and its mechanistic implications are discussed as well.</div>

scholarly journals Affinity and Specificity of Protein U1A-RNA Complex Formation Based on an Additive Component Free Energy Model

2007 ◽  
Vol 371 (5) ◽  
pp. 1405-1419 ◽  
Author(s):  
Bethany L. Kormos ◽  
Yulia Benitex ◽  
Anne M. Baranger ◽  
David L. Beveridge
Keyword(s):  
Free Energy ◽  
Complex Formation ◽  
Energy Model ◽  
Additive Component ◽  
Free Energy Model ◽  
Rna Complex

A Two-Dimensional Free Energy Model for Single Crystalline Ferroelectrics

2005 ◽  
Vol 881 ◽  
Author(s):  
Sang-Joo Kim ◽  
Stefan Seelecke ◽  
Brian L. Ball ◽  
Ralph C. Smith ◽  
Chang-Hoan Lee
Keyword(s):  
Free Energy ◽  
Evolution Equations ◽  
Saddle Points ◽  
Ferroelectric Materials ◽  
Energy Model ◽  
Two Dimensions ◽  
Two Dimensional ◽  
Energy Potential ◽  
Single Crystalline ◽  
Free Energy Model

AbstractThe one-dimensional free energy model for ferroelectric materials developed in [1-3] is general-ized to two dimensions. The proposed two-dimensional energy potential consists of four energy wells corresponding to four variants of the material, four saddle points representing the barriers for 900 switching processes, and a local energy maximum across which 1800-switching processes take place. The free energy potential is combined with the evolution equations based on the theory of thermally activated processes. The prediction of the model is compared with the recent measurements on a Ba- TiO3 single crystalline ferroelectric in [4]. The responses of the model at various loading frequencies are calculated and the kinetics of 900 and 1800 switching processes are discussed.

Dangling Bonds in Amorphous Silicon Nitride Alloys: Predictions of the Free Energy Model

1992 ◽  
Vol 284 ◽  
Author(s):  
F. W. Smith ◽  
H. Efstathiadis ◽  
Z. Yin
Keyword(s):  
Free Energy ◽  
Energy Gap ◽  
Energy Levels ◽  
Experimental Studies ◽  
Energy Model ◽  
Paramagnetic Defect ◽  
Amorphous Network ◽  
Energy Of Mixing ◽  
Free Energy Model ◽  
Free Energy Of Mixing

ABSTRACTThe free energy model (FEM) for bonding in a-SixNyHz alloys has been extended to include the contributions of neutral and charged Si and N defects to the free energy of mixing of the amorphous alloy. The FEM predicts that the dominant defects in N-rich alloys are N2o, N2-, and either S3+ or N2+, in contrast to the results of experimental studies that find the dominant neutral, paramagnetic defect to be Si3o. It is concluded that either the observed Si3o defects are not in thermodynamic equilibrium with the amorphous network or the N2o defects have energy levels which lie much higher in the energy gap than currently believed.

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